rs136501

Variant names:

• chr22-26839368-T-C
• rs136501
• ENST00000450963.6:n.1169-12541T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000716994.1(MIATNB):​n.691-12541T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,084 control chromosomes in the GnomAD database, including 5,403 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (5403 hom., cov: 32)
• Consequence: MIATNB ENST00000716994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 1 publications found

Genes affected

MIATNB (HGNC:50731): (MIAT neighbor)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716994.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIATNB	ENST00000450963.6	TSL:5	n.1169-12541T>C		intron	N/A
	MIATNB	ENST00000716994.1		n.691-12541T>C		intron	N/A
	MIATNB	ENST00000716995.1		n.705-22614T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34857 AN: 151966 Hom.: 5381 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0900

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.190

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.230 AC: 34928 AN: 152084 Hom.: 5403 Cov.: 32 AF XY: 0.227 AC XY: 16850 AN XY: 74350

African (AFR) AF: 0.428 AC: 17752 AN: 41432

American (AMR) AF: 0.270 AC: 4121 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1557 AN: 5158

South Asian (SAS) AF: 0.117 AC: 564 AN: 4826

European-Finnish (FIN) AF: 0.0900 AC: 954 AN: 10598

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8819 AN: 68012

Other (OTH) AF: 0.190 AC: 400 AN: 2110

Alfa AF: 0.180 Hom.: 449

Bravo AF: 0.255

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.57
PhyloP100		-1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs136501; hg19: chr22-27235331;